Investigation on DNA assembly to neutral red-cyclodextrin complex by molecular spectroscopy

DNA assembling to neutral red (NR) and cyclodextrins (CDs)-NR inclusion complex has been investigated by means of absorption, fluorescence and resonance light scattering (RLS). Depending on the molar ratio R of NR:DNA, the binding of NR with DNA involved in two processes at pH 7.50 and ionic strength 0.0045. The first process occurs in R>2.5, where the neutral form of NR was predominant and enhanced RLS was observed, indicating the aggregation of NR neutral form molecules on the molecular surface of DNA. The second process occurs in R<2.5, where an absorption band at 540 nm and a fluorescent excitation and emission band at 550 and 607 nm respectively provided compelling evidence that the binding of NR to DNA leaded to extensive NR protonation even at pH 7.50, and that a protonated NR (the acidic form of NR) can form DNA adducts with a binding mode different from that of the unprotonated form (the neutral form of NR). The results were also illustrated by the CDs-NR supramolecular system. The experimental data showed that CDs including beta-CD, hydroxypropyl-beta-CD (HP-beta-CD) and sulfobutylether-beta-CD (SBE-beta-CD) superior to include the neutral form of NR, in addition, the inclusion complex decomposed when it bound to DNA. Thus, the decomposed NR was also protonated to form DNA adducts with intercalative mode. In fact, CDs played a role to carry guest molecule to intercalate DNA. A related mechanism is proposed.